Homology alignment of shRNA E1 target sequence to the CHIKV genome of several geographical isolates.

Nucleotide BLAST sequence analysis of shRNA E1 target site sequence (Query) to the genomic sequence (Sbjct) of the various geographical strains of CHIKV revealed 100% homology of the target site to the respective E1 gene sequence (except one base pair mismatch to the S27-African prototype, Singapore LK(EH)CH6708 and Malaysia MY002IMR/06/BP strains. The mismatched base is bold and underlined). An additional AA dinucleotide was incorporated to the 5′ end of the 19-mer shRNA to obtain an effective 21-mer shRNA construct. Alignment data for shRNA Capsid and shRNA nsP1 are not shown. aNucleotide position of the Sbjct sequence in the CHIKV genome.